Microbial Diversity of Some Sabkha and Desert Sites in Saudi Arabia

Abstract

Several studies isolated fungal and bacterial species from extreme environments, such as Sabkha and hot deserts, as their natural habitat, some of which are of medicinal importance. Current research aimed investigating the microbial (fungi and bacteria) diversity and abundance in Sabkha and desert areas in Saudi Arabia. Soil samples from nine different geographical areas (Al-Aushazia lake, AlQasab, AlKasar, Tabuk, Al-Kharj, Al-Madina, Jubail, Taif and Abqaiq) were collected and cultured for microbial isolation. Isolated fungi and bacteria were identified by molecular techniques (PCR and sequencing). Based on 18S rDNA sequencing, 203 fungal species belonging to 33 genera were identified. The most common fungal genera were Fusarium, Alternaria, Chaetomium, Aspergillus Cochliobolus and Pencillium, while the most common species were Chaetomium globosum and Fusarium oxysporum. By 16S rDNA sequencing 22 bacterial species belonging to only two genera, Bacillus and Lactobacillus, were identified. The most commonly isolated bacterial species were Bacillus subtilis and Lactobacillus murinus. Some fungal species were confined to specific locations, such as Actinomyces elegans, Fusarium proliferatum, Gymnoascus reesii and Myzostoma spp. that were only isolated from Al-Aushazia soil. AlQasab soil had the highest microbial diversity among other areas with abundances of 23.5% and 4.4% of total fungi, and bacteria, respectively. Findings of this study show a higher degree of fungal diversity than that of bacteria in all studied areas. Further studies needed to investigate the connection between some isolated species and their habitat ecology, as well as to identify those of medicinal importance.

Keywords: Desert; Ecology; Microbial diversity; Molecular; Sabkha; Saudi Arabia; Soil.

Fig. 1

The locations investigated.

Fig. 2

Microbial abndance in all study sites, (a) is the fungi and (b) bacteria.

Fig. 3

Images of study area of AlQasab (a) and the soil particle size (b) detected using SEM at a magnification of 10.00. The scale bar represents 500 μm.

Fig. 4

Images of study site of Taif (a) and the soil particle size (b) detected using SEM at a magnification of 10.00. The scale bar represents 500 μm.

Fig. 5

Images of study site of Al-Aushazia lake (a) and the soil particle size (b) detected using SEM at a magnification of 20.00. The scale bar represents 500 μm.

Fig. 6

Images of study site of Tabuk (a) and the soil particle size (b) detected using SEM at a magnification of 20.00. The scale bar represents 500 μm.

Fig. 7

Images of study site of Jubail (a) and the soil particle size (b) detected using SEM at a magnification of 10.00. The scale bar represents 500 μm.

Fig. 8

Images of study site of Al-Kharj (a) and the soil particle size (b) detected using SEM at a magnification of 10.00 and scale bar represents 500 μm.

Fig. 9

Images of study site of Al-Kasr (a) and the soil particle size (b) detected using SEM at a magnification of 10.00 and scale bar represents 500 μm.

Fig. 10

Images of study site of Al-Madina (a) and the soil particle size (b) detected using SEM at a magnification of 10.00 and scale bar represents 500 μm.

Fig. 11

Images of study site of Abqaiq (a) and the soil particle size (b) detected using SEM at a magnification of 10.00 and scale bar represents 500 μm.

Fig. 12

Phylogenetic relationships among Bacterial isolates were used for constructing the phylogenetic tree including the corresponding species, Bacillus paralicheniformis (CP020352), Bacillus velezensis (CP041361) and Bacillus subtilis (CP018173). 16S rDNA sequences were aligned using ClustalW. A Neighbor-joining method was used to build the tree with 1000 bootstraps by MEGA X. The GenBank accession No. of the 16SrDNA sequences used for phylogenetic tree analysis are indicated at the end of each branch (given the MT Numbers). The Escherichia coli (GenBank accession number NR 024570) is used as outgroup. Numbers shown next to the branches display percentage of bootstrap values. Scale bar specified nucleotide substitutions per site.

Fig. 13

Phylogenetic tree for fungal species isolated from nine sites in Saudi Arabia based on 18SrDNA sequences were used for constructing the phylogenetic tree (including the corresponding species from NCBI, indicated with GenBank accession number at the tip of each branch). 18S rDNA sequences were aligned using MUSCLE. A Neighbor-joining tree was conducted using MEGAX with 1000 bootstrap replicates according to Kimura 2-parameter model. The GenBank accession No. of the 18S rDNA sequences isolates in this study are indicated at the end of each branch (given the MN Numbers). The Mortierella parvispora strain CBS 311.52 (GenBank accession number MH868588) was used as outgroup. Numbers shown next to the branches display percentage of bootstrap values. Scale bar specified nucleotide substitutions per site.